Development, maintenance and sharing of small-scale databases for genome research

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Development, maintenance and sharing of
small-scale databases for genome research

• Volker Brendel
• Department of Genetics, Development and Cell
  Biology
• Department of Statistics
• Iowa State University

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the joys and perils of molecular data mining
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http//genome-www5.stanford.edu/MicroArray/SMD/
Blader IJ, et al. (2001) J Biol Chem
276(26)24223-31 Microarray Analysis Reveals
Previously Unknown Changes in Toxoplasma
gondii-infected Human Cells.
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The Molecular Biology Database Collection 2003
update Andreas D. Baxevanis
Database Categories List Major Sequence
Repositories Comparative Genomics Gene
Expression Gene Identification and Structure
Genetic and Physical Maps Genomic Databases
Intermolecular Interactions Metabolic Pathways
and Cellular Regulation Mutation Databases
Pathology Protein Databases Protein Sequence
Motifs Proteome Resources RNA Sequences
Retrieval Systems and Database Structure
Structure Transgenics Varied Biomedical Content
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Alphabetical Database List
 
16S and 23S Ribosomal RNA Mutation Database   
AAindex
Physicochemical properties of peptides
ACeDB
C. elegans, S. pombe, and human sequences and
genomic information

. . .
ZmDB

Maize genome database
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Molecular Databases - Problems

• Content (accuracy currency)
• Multiplicity (gt 1,000 specialized databases!?)
• Lack of standards (e.g., ZmDB ACeDB, MySQL,
  FileMakerPro)
• Accessibility (web!?)

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Why are there so many distinct databases in
molecular biology?
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NSF 99 -171 PLANT GENOME RESEARCH PROGRAM -
COLLABORATIVE RESEARCH ON FUNCTIONAL GENOMICS
Program Announcement DIRECTORATE FOR BIOLOGICAL
SCIENCES LETTER OF INTENT NOVEMBER 8, 1999
PROPOSAL DEADLINE JANUARY 7, 2000
                NATIONAL SCIENCE FOUNDATION
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• Informatics Include a detailed description of
  all informatics components of the project. This
  section should describe the informatics tools
  used for internal data management as well as the
  distribution of information to the scientific
  community. Technical descriptions must be
  sufficiently detailed to allow adequate review by
  informatics experts. All data must be released to
  the public in an accessible and useable form. If
  project includes development of a new database or
  expansion of an existing database, a plan for its
  long-term maintenance must be described.

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Case studyZmDB a maize genome database

• www.zmdb.iastate.edu

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End of funding!End of project!?End of
database!?End of data integrity!?
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MaizeGDB

• www.maizedb.org

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Case studyZmDB one need leads to many others
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PlantGDB

• www.plantgdb.org

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Data integrityProblems and possible solutions
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AtGDB

• www.plantgdb.org/AtGDB

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Matt Wilkerson
Shannon Schlueter
NSF Plant Genome Research Project(s)
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Genome Annotation The Need for User
Contributions! Examples for Arabidopsis
At1g28080 (missed 5' UTR)
At2g40840 (intergenic region? U12 intron!)
User Contributed Annotation Alan Myers!?
At1g14370 (overlapping 3'-UTRs ? no!)
User Contributed Annotation Your Name here!!